All perfect praise be to Allaah, The Lord of the Worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad is His slave and Messenger.
Al-Bukhari reported 'Aa'ishah as having said that the Prophet had said: "There is healing in the black seed for every disease except death." [Al-Bukhari and Muslim].
As for the manner of using it as a healing agent, there is no particular way. In his book 'Fath al-Bari', Ibn Hajar said,
"Al-Mustaghfiri in his 'Book of Medicine' reported Ibn Buraidah as having quoted the Prophet saying: 'There is healing in the black seed…etc.'
In another narration it was said, 'What is the black seed?' He said, 'Shoneez' (a name for black seed; scientific name Nigella sativa).
Someone then asked, 'How can I use it?' to which he answered: You take twenty one grains (black seeds) and put them in a piece of cloth then in water for one night. When you get up in the following morning, you drop one drop in your right nostril and two in your left nostril".
Al-Haafith (Ibn Hajar ) said, "What is to be understood from this Hadeeth about the black seed being a healing for every disease is that it is not necessarily applied alone as a treatment procedure for every case. Rather it may be used alone, in combination with something else, pulverized, directly without pulverizing it, mixed with food and drink, or as dressing, etc."
Allaah Knows best.